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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15

To enhance the AlphaFold-Multimer-based protein complex structure prediction, we developed a quaternary structure prediction system (MULTICOM) to improve the input fed to AlphaFold-Multimer and evaluate and refine its outputs. MULTICOM samples diverse multiple sequence alignments (MSAs) and templates for AlphaFold-Multimer to generate structural predictions by using both traditional sequence alignments and Foldseek-based structure alignments, ranks structural predictions through multiple complementary metrics, and refines the structural predictions via a Foldseek structure alignment-based refinement method. The MULTICOM system with different implementations was blindly tested in the assembly structure prediction in the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022 as both server and human predictors. MULTICOM_qa ranked 3 rd among 26 CASP15 server predictors and MULTICOM_human ranked 7 th among 87 CASP15 server and human predictors. The average TM-score of the first predictions submitted by MULTICOM_qa for CASP15 assembly targets is ~0.76, 5.3% higher than ~0.72 of the standard AlphaFold-Multimer. The average TM-score of the best of top 5 predictions submitted by MULTICOM_qa is ~0.80, about 8% higher than ~0.74 of the standard AlphaFold-Multimer. Moreover, the Foldseek Structure Alignment-based Multimer structure Generation (FSAMG) method outperforms the widely used sequence alignment-based multimer structure generation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Electric-field-induced structure and domain texture evolution in PbZrO 3 -based antiferroelectric by in-situ high-energy synchrotron X-ray diffraction

Antiferroelectrics (AFEs) have a great potential for modern electronic devices by virtue of the large strain during the antiferroelectric-to-ferroelectric (AFE-FE) phase transition under external electric fields. Although the fascinating macroscopic properties of AFE materials have been extensively studied, it is still unclear how the underlying structure evolution engenders their defining properties. Here we employ an electric biasing in-situ high-energy synchrotron X-ray diffraction technique to reveal the phase, domain texture, and lattice evolution in a high performance PbZrO 3 -based AFE material. During the reversible AFE-FE transition triggered by electric fields, the evolution of the superstructure for AFE pseudo-tetragonal and FE rhombohedral phase is found to display strong dependence on the angle with respect to the field direction. In contrast to previous prediction, it is found that there is no obvious domain reorientation in the AFE phase, when the system is far away from the AFE-FE transitions. The electric-field-induced FE rhombohedral phase exhibits an unusual microscopic behavior, distinguished from the normal one, presenting small changes in domain texture and lattice strain with electric field, and leading to a small piezoelectric response. The longitudinal, transverse, and volume strains estimated from the XRD peak profiles are well consistent with the macroscopic strain measurements. It is demonstrated that the large strain arises from the structural change associated with anisotropic lattice strain and highly preferential domain reorientation during the AFE-FE transitions. Finally, the AFE-FE switching sequence is constructed based on the present study, which provides a further understating of AFE materials.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Functional characterization of a cellulose synthase, CtCESA1, from the marine red alga Calliarthron tuberculosum (Corallinales)

In land plants and algae, cellulose is important for strengthening cell walls and preventing breakage due to physical forces. Though our understanding of cellulose production by cellulose synthases (CESAs) has seen significant advances for several land plant and bacterial species, functional characterization of this fundamental protein is absent in red algae. Here we identify CESA gene candidates in the calcifying red alga Calliarthron tuberculosum using sequence similarity-based approaches, and elucidate their phylogenetic relationship with other CESAs from diverse taxa. One gene candidate, CtCESA1, was closely related to other putative red algal CESA genes. To test if CtCESA1 encoded a true cellulose synthase, CtCESA1 protein was expressed and purified from insect and yeast expression systems. CtCESA1 showed glucan synthase activity in glucose tracer assays. CtCESA1 activity was relatively low when compared with plant and bacterial CESA activity. In an in vitro assay, a predicted N-terminal starch-binding domain from CtCESA1 bound red algal floridean starch extracts, representing a unique domain in red algal CESAs not present in CESAs from other lineages. When the CtCESA1 gene was introduced into Arabidopsis thaliana cesa mutants, the red algal CtCESA1 partially rescued the growth defects of the primary cell wall cesa6 mutant, but not cesa3 or secondary cell wall cesa7 mutants. A fluorescently tagged CtCESA1 localized to the plasma membrane in the Arabidopsis cesa6 mutant background. This study presents functional evidence validating the sequence annotation of red algal CESAs. Furthermore, the relatively low activity of CtCESA1, partial complementation in Arabidopsis, and presence of unique protein domains suggest that there are probably functional differences between the algal and land plant CESAs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Epigenetic regulation leading to induced pluripotency drives cancer development in vivo

Highlights: • Epigenetic regulation of failed reprogramming-associated cancer cells is discussed. • Similarity between pediatric cancer and reprogramming-associated cancer is discussed. • Concept for epigenetic cancer is discussed. - Abstract: Somatic cells can be reprogrammed into induced pluripotent stem cells (iPSCs) by the transient expression of reprogramming factors. During the reprogramming process, somatic cells acquire the ability to undergo unlimited proliferation, which is also an important characteristic of cancer cells, while their underlying DNA sequence remains unchanged. Based on the characteristics shared between pluripotent stem cells and cancer cells, the potential involvement of the factors leading to reprogramming toward pluripotency in cancer development has been discussed. Recent in vivo reprogramming studies provided some clues to understanding the role of reprogramming-related epigenetic regulation in cancer development. It was shown that premature termination of the in vivo reprogramming result in the development of tumors that resemble pediatric cancers. Given that epigenetic modifications play a central role during reprogramming, failed reprogramming-associated cancer development may have provided a proof of concept for epigenetics-driven cancer development in vivo.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2009

A Comprehensive Characterization of Microorganisms and Allergens in Spacecraft Environment

The determination of risk from infectious disease during long-duration missions is composed of several factors including the concentration and the characteristics of the infectious agent. Thus, a thorough knowledge of the microorganisms aboard spacecraft is essential in mitigating infectious disease risk to the crew. While stringent steps are taken to minimize the transfer of potential pathogens to spacecraft, several medically significant organisms have been isolated from both the Mir and International Space Station (ISS). Historically, the method for isolation and identification of microorganisms from spacecraft environmental samples depended upon their growth on culture media. Unfortunately, only a fraction of the organisms may grow on a culture medium, potentially omitting those microorganisms whose nutritional and physical requirements for growth are not met. Thus, several pathogens may not have been detected, such as Legionella pneumophila, the etiological agent of Legionnaire s disease. We hypothesize that environmental analysis using non-culture-based technologies will reveal microorganisms, allergens, and microbial toxins not previously reported in spacecraft, allowing for a more complete health assessment. The development of techniques for this flight experiment, operationally named SWAB, has already provided advances in NASA laboratory processes and beneficial information toward human health risk assessment. The translation of 16S ribosomal DNA sequencing for the identification of bacteria from the SWAB experiment to nominal operations has increased bacterial speciation of environmental isolates from previous flights three fold compared to previous conventional methodology. The incorporation of molecular-based DNA fingerprinting using repetitive sequence-based polymerase chain reaction (rep-PCR) into the capabilities of the laboratory has provided a methodology to track microorganisms between crewmembers and their environment. Both 16S ribosomal DNA identification and bacterial fingerprinting have improved NASA s capability to better understand spacecraft environments and determine the source of contamination events. Preflight sampling has been completed for air, surface, and water samples. In-flight sample collection has been completed for a total of 8 air and surface sample collection sessions. In-flight hardware has performed well and the surface sampling device received positive feedback from the crew for its ease of use. While processing and analysis continue for these samples, early results have begun to provide information on the spacecraft environment. Using a method called Denaturing Gradient Gel Electrophoresis (DGGE), several air and samples were evaluated to determine the types of organisms that were present. Using only molecular techniques, DGGE does not depend on any microbial growth on culture media, allowing a more comprehensive assessment of the spacecraft interior. Preliminary results have identified several microorganisms that would not have been isolated using current technology, though none of these organisms would be considered medically significant. Interestingly, the isolation of Gram negative organisms is greater using DGGE than conventional media based isolation. The cause of this finding is unclear, though it may be the result of the technique s ability to isolate both viable and non-viable bacteria. The next phase of the SWAB sample analysis is the use of quantitative polymerase chain reaction (QPCR) to look for specific medically significant organisms. While not as broad as DGGE, QPCR is much more sensitive and may reveal findings that were not seen during the initial evaluation. Together, this information will lead toward an accurate microbial risk assessment to help set flight requirements to protect the safety, health, and performance of the crew.

Castro, V.A.↗
DOE OSTI2014

TH-E-17A-04: Geometric Validation of K-Space Self-Gated 4D-MRI Vs. 4D-CT Using A Respiratory Motion Phantom

Purpose: 4D-CT is often limited by motion artifacts, low temporal resolution, and poor phase-based target definition. We recently developed a novel k-space self-gated 4D-MRI technique with high spatial and temporal resolution. The goal here is to geometrically validate 4D-MRI using a MRI-CT compatible respiratory motion phantom and comparison to 4D-CT. Methods: 4D-MRI was acquired using 3T spoiled gradient echo-based 3D projection sequences. Respiratory phases were resolved using self-gated k-space lines as the motion surrogate. Images were reconstructed into 10 temporal bins with 1.56×1.56×1.56mm3. A MRI-CT compatible phantom was designed with a 23mm diameter ball target filled with highconcentration gadolinium(Gd) gel embedded in a 35×40×63mm3 plastic box stabilized with low-concentration Gd gel. The whole phantom was driven by an air pump. Human respiratory motion was mimicked using the controller from a commercial dynamic phantom (RSD). Four breathing settings (rates/depths: 10s/20mm, 6s/15mm, 4s/10mm, 3s/7mm) were scanned with 4D-MRI and 4D-CT (slice thickness 1.25mm). Motion ground-truth was obtained from input signals and real-time video recordings. Reconstructed images were imported into Eclipse(Varian) for target contouring. Volumes and target positions were compared with ground-truth. Initial human study was investigated on a liver patient. Results: 4D-MRI and 4D-CT scans for the different breathing cycles were reconstructed with 10 phases. Target volume in each phase was measured for both 4D-CT and 4D-MRI. Volume percentage difference for the 6.37ml target ranged from 6.67±5.33 to 11.63±5.57 for 4D-CT and from 1.47±0.52 to 2.12±1.60 for 4D-MRI. The Mann-Whitney U-test shows the 4D-MRI is significantly superior to 4D-CT (p=0.021) for phase-based target definition. Centroid motion error ranges were 1.35–1.25mm (4D-CT), and 0.31–0.12mm (4D-MRI). Conclusion: The k-space self-gated 4D-MRI we recently developed can accurately determine phase-based target volume while avoiding typical motion artifacts found in 4D-CT, and is being further studied for use in GI targeting and motion management. This work supported in part by grant 1R03CA173273-01.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

High-resolution phylogenetic microbial community profiling

The representation of bacterial and archaeal genome sequences is strongly biased towards cultivated organisms, which belong to merely four phylogenetic groups. Functional information and inter-phylum level relationships are still largely underexplored for candidate phyla, which are often referred to as microbial dark matter. Furthermore, a large portion of the 16S rRNA gene records in the GenBank database are labeled as environmental samples and unclassified, which is in part due to low read accuracy, potential chimeric sequences produced during PCR amplifications and the low resolution of short amplicons. In order to improve the phylogenetic classification of novel species and advance our knowledge of the ecosystem function of uncultivated microorganisms, high-throughput full length 16S rRNA gene sequencing methodologies with reduced biases are needed. We evaluated the performance of PacBio single-molecule real-time (SMRT) sequencing in high-resolution phylogenetic microbial community profiling. For this purpose, we compared PacBio and Illumina metagenomic shotgun and 16S rRNA gene sequencing of a mock community as well as of an environmental sample from Sakinaw Lake, British Columbia. Sakinaw Lake is known to contain a large age of microbial species from candidate phyla. Sequencing results show that community structure based on PacBio shotgun and 16S rRNA gene sequences is highly similar in both the mock and the environmental communities. Resolution power and community representation accuracy from SMRT sequencing data appeared to be independent of GC content of microbial genomes and was higher when compared to Illumina-based metagenome shotgun and 16S rRNA gene (iTag) sequences, e.g. full-length sequencing resolved all 23 OTUs in the mock community, while iTags did not resolve closely related species. SMRT sequencing hence offers various potential benefits when characterizing uncharted microbial communities.

09 BIOMASS FUELS↗
DOE OSTI2017

Electrochemical Energy Storage with a Reversible Nonaqueous Room-Temperature Aluminum-Sulfur Chemistry

A reversible room-temperature aluminum–sulfur (Al-S) battery is demonstrated with a strategically designed cathode structure and an ionic liquid electrolyte. Discharge–charge mechanism of the Al-S battery is proposed based on a sequence of electrochemical, microscopic, and spectroscopic analyses. The electrochemical process of the Al-S battery involves the formation of a series of polysulfides and sulfide. The high-order polysulfides (S x 2- , x ≥ 6) are soluble in the ionic liquid electrolyte. Electrochemical transitions between S 6 2 - and the insoluble low-order polysulfides or sulfide (S x 2- , 1 ≤ x < 6) are reversible. A single-wall carbon nanotube coating applied to the battery separator helps alleviate the diffusion of the polysulfide species and reduces the polarization behavior of the Al-S batteries.

25 ENERGY STORAGE↗
DOE OSTI2017

1 H- 19 F REDOR-filtered NMR spin diffusion measurements of domain size in heterogeneous polymers

Solid state NMR spectroscopy is inherently sensitive to chemical structure and composition, and thus makes an ideal method to probe the heterogeneity of multicomponent polymers. Specifically, NMR spin diffusion experiments can be used to extract reliable information about spatial domain sizes on multiple length scales, provided that magnetization selection of one domain can be achieved. In this paper, we demonstrate the preferential filtering of protons in fluorinated domains during NMR spin diffusion exper-iments using 1 H- 19 F heteronuclear dipolar dephasing based on rotational echo double resonance (REDOR) MAS NMR techniques. Three pulse sequence variations are demonstrated based on the different nuclei detected: direct 1 H detection, plus both 1 H→ 13 C cross polarization (CP) and 1 H→ 19 F CP detection schemes. This 1 H- 19 F REDOR-filtered spin diffusion method was used to measure fluorinated domain sizes for a complex polymer blend. The efficacy of the REDOR-based spin filter does not rely on spin relaxation behavior or chemical shift differences, and thus is applicable for performing NMR spin diffu-sion experiments in samples where traditional magnetization filters may prove unsuccessful. This REDOR-filtered NMR spin diffusion method can also be extended to other samples where a heteronuclear spin pair exists that is unique to the domain of interest.

36 MATERIALS SCIENCE↗
DOE OSTI2020

High‐order cubature rules for tetrahedra

Summary In this paper, we construct new high‐order numerical integration schemes for tetrahedra, with positive weights and integration points that are in the interior of the domain. The construction of cubature rules is a challenging problem, which requires the solution of strongly nonlinear algebraic (moment) equations with side conditions given by affine inequality constraints. We present a robust algorithm based on a sequence of three modified Newton procedures to solve the constrained minimization problem. In the literature, numerical integration rules for the tetrahedron are available up to order p =15. We obtain integration rules for the tetrahedron from p =2 to p =20, which are computed using multiprecision arithmetic. For p ≤15, our approach provides integration rules that have the same or fewer number of integration points than existing rules; for p =16 to p =20, our rules are new. Numerical tests are presented that verify the polynomial‐precision of the cubature rules. Convergence studies are performed for the integration of exponential, rational, weakly singular and trigonometric test functions over tetrahedra with flat and curved faces. In all tests, improvements in accuracy is realized as p is increased, though in some cases nonmonotonic convergence is observed.

Jaśkowiec, Jan↗
DOE OSTI2026

Small Signaling Peptides in Sorghum bicolor : Integrating Phylogeny and Gene Expression to Characterize Roles in Stem Development

Small signaling peptides (SSPs) are important regulators of plant growth, development, and responses to biotic and abiotic stress, yet their role in the C4 grass Sorghum bicolor is largely uncharacterized. To help fill this knowledge gap, 219 sorghum genes that encode SSPs were identified based on SSP sequences previously identified in Arabidopsis thaliana, Zea mays, Oryza sativa, Triticum aestivum , and Brachypodium distachyon . The 219 sorghum SSP-encoding genes were assigned to 19 gene families, analyzed for the presence of motifs, and aligned with genes that encode SSPs in other plants using phylogenetic analysis. Sorghum genes in 12 of the 19 SSP gene families had not been previously characterized. Expression of the 219 SSP-encoding genes in sorghum organs, during stem development, and in stem tissues and cell types revealed distinct spatial, temporal, and developmental patterns of expression. Genes associated with the SbCEP and SbRGF families were preferentially expressed in roots, whereas SbEPF genes were expressed in stem epidermal and pith parenchyma cells and panicles. The expression of genes during bioenergy sorghum stem growth and development was investigated because stems account for ~80% of harvested biomass and serve as conduits for water and nutrient transport between leaves and roots. During stem development, 28 SSP genes in several families ( CLE, EPF, CEP, GASS, PSY, ES, PSK, CAPE, POE ) were expressed at higher levels in zones of cell proliferation. For example, the TDIF homologs SbCLE41 and SbCLE42 were expressed at high levels in nascent stem nodes where they may regulate vascular bundle cambial activity and cell differentiation. A different set of 15 genes in the CIF, POE, CAPE, PSY, CEP, RALF , and CLE families were expressed at higher levels in zones of stem tissue differentiation highlighted by elevated expression of five SbRALFR s in the stem nodal plexus. Cell type–specific expression of many sorghum genes that encode SSPs was observed in fully elongated internodes indicating gene expression is regulated with high spatial resolution. Overall, the results provide a foundation of information for analysis of SSP function in sorghum that can be integrated with knowledge of sorghum gene regulatory networks to modulate traits important for production of sorghum crops.

bioenergy sorghum↗
DOE OSTI2020

Molecular remodeling in Populus PdKOR RNAi roots profiled using LC-MS/MS proteomics

Plant endo-β-1,4-glucanases belonging to the Glycoside Hydrolase Family 9 have functional roles in cell wall biosynthesis and remodeling via endohydrolysis of (1→4)-β-D-glucosidic linkages. Modification of cell wall chemistry via RNAi-mediated downregulation of Populus deltoides KOR1 (PdKOR), a endo-β-1,4-glucanase gene, in Populus deltoides has been shown to have functional consequences for the composition of secondary metabolome and the ability of modified roots to interact with beneficial microbes. The molecular remodeling that underlies the observed differences at metabolic, physiological, and morphological levels in roots is not well understood. Here we used a LC-MS/MS-based proteome profiling approach to survey the molecular remodeling in root tissues of PdKOR and control plants. A total of 14316 peptides were identified and these mapped to 7139 P. deltoides proteins. Based on 90% sequence identity, the measured protein accessions represent 1187 functional protein groups. Analysis of GO categories and specific individual proteins showed differential expression of proteins relevant to plant-microbe interactions, cell wall chemistry, and metabolism. The new proteome dataset serves as a useful resource for deriving new hypotheses and empirical testing pertaining to functional roles of proteins and pathways in differential priming of plant roots to interactions with microbes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Natural and targeted isovariants of the rice actin depolymerizing factor 2 can alter its functional and regulatory binding properties

Highlights: • Single site mutations in rice ADF2 alter its structure and actin binding, bundling, depolymerizing activity of the protein. • Serine-6>threonine mutation attenuates phosphorylation by calcium dependent protein kinase. • N-terminal mutations affect phosphorylation pattern while C-terminal mutations affect actin binding and severing. Actin depolymerizing factors (ADFs) are ubiquitous actin-binding proteins that play essential roles in maintaining cellular actin dynamics by depolymerizing/severing F-actin. Plant ADF isoforms show functional divergence via differential biochemical and cellular properties. We have shown previously that ADF2 of rice (OsADF2) and smooth cordgrass (SaADF2) displayed contrasting biochemical properties and stress response in planta. As a proof-of-concept that amino acid variances contribute to such functional difference, single amino acid mutants of OsADF2 were generated based on its sequence differences with SaADF2. Biochemical studies showed that the single-site amino acid mutations altered actin binding, depolymerizing, and severing properties of OsADF2. Phosphosensitive mutations, such as serine-6>threonine, changed the regulatory phosphorylation efficiency of ADF{sub 2} variants. The N-terminal mutations had greater effect on the phosphorylation pattern of OsADF2, whereas C-terminal mutations affected actin binding and severing. The presence of introduced mutations in isovariants of monocot ADF suggests that these residues are significant control points regulating their functional divergence, including abiotic stress response.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Characterization of a novel ω-transaminase from a Triassic salt mine metagenome

Highlights: • Metagenome derived from hypersaline environment, formed during Triassic Period. • Novel and active ω-transaminase enzyme synthesized from environmental DNA. • Molecular modeling and docking simulations reveal equivalents to mesophilic enzymes. • Characterization shows different profile to previous halophilic transaminases. Chiral amines are valuable building blocks for the pharmaceutical industry, and are increasingly synthesized by transaminase-mediated (TAm) synthesis. Currently available TAms, primarily isolated from the genomes of cultured mesophilic bacteria, often suffer from a number of drawbacks, including poor substrate range and an inability to tolerate the harsh conditions often demanded by industrial processes. These characteristics have, in part, driven the search for novel biocatalysts from both metagenomic sources and extreme environments. Herein, we report the isolation and characterization of an ω-TAm from a metagenome of a Triassic salt mine in Kilroot, N. Ireland, an extremely hypersaline environment formed circa 220–250 mya. The gene sequence was identified based on homology with existing bacterial TAms, synthesized within a pET28a(+) plasmid and expressed in E. coli BL21 DE3 cells. The resultant 49 kDa protein accepted (S)-methylbenzylamine (MBA) as amino donor and had a specific activity of 0.54 U/mg using α-ketoglutarate (ΑKG) as substrate. Molecular modeling and substrate docking indicated the presence of key residues, conserved in a number of other TAms. Despite the hypersaline environment from which it was isolated, the enzyme displayed low halotolerance, highlighting that not all biocatalysts will demonstrate the extreme characteristics associated with their source environment. This study does however reinforce the viability of mining metagenomic datasets as a means of discovering novel and functional biocatalysts, and adds to a currently scant list of such examples in the field of TAms.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Helicobacter pylori flagellin: TLR5 evasion and fusion-based conversion into a TLR5 agonist

Highlights: • Helicobacter flagellin (hFlg) evades TLR5 by modifying a TLR5-activation hot spot. • The hypervariable domains of hFlg were identified as the soluble part of hFlg. • hFlg was engineered to activate TLR5 through fusion with Bacillus flagellin. Helicobacter pylori is a flagellated bacterium of the Epsilonproteobacteria class that causes peptic ulcers. Flagellin is a primary structural protein that assembles into the flagellar filament. Flagellins from bacteria that belong to the Gammaproteobacteria and Firmicutes groups are detected by Toll-like receptor 5 (TLR5) in the host, triggering the innate immune response, and thus have been studied for the development of vaccines against diverse infections through fusion with protein antigens. However, H. pylori flagellin (hFlg) does not stimulate TLR5, allowing H. pylori to evade TLR5-mediated immune surveillance. The unresponsiveness of TLR5 to hFlg, along with the tendency of the hFlg protein to precipitate, limits the utility of hFlg for H. pylori vaccine development. Here, we report a soluble hFlg derivative protein that activates TLR5. We performed expression and purification screens with full-length and fragment hFlg proteins and identified the hypervariable domains as the soluble part of hFlg. The hypervariable domains of hFlg were engineered into a TLR5 agonist through fusion with the TLR5-activating Bacillus subtilis flagellin. Furthermore, based on comparative sequence and mutation analyses, we reveal that hFlg evolved to evade TLR5 detection by modifying residues that correspond to a TLR5-activation hot spot.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Combining direct ink writing with reactive melt infiltration to create architectured thermoelectric legs

Here, we present a new additive-reactive synthesis method where inks – cast into molds or 3D-additively extruded into architectured shapes – are reacted into intermetallic thermoelectric compounds. The new method, as demonstrated for equiatomic TiNiSn, combines: (i) extrusion printing (or casting) of inks containing Ni and Ti powders, (ii) debinding and reactive sintering to form a porous NiTi network, (iii) network infiltration with liquid Sn and subsequent reaction to synthesize the TiNiSn phase. Thin plates, created through this method, show high phase purity and low residual porosity. A thermoelectric figure of merit zT = 0.47 ± 0.05 is achieved at 800 K, within the broad range of values (zT= 0.3–1.0) reported for TiNiSn created via traditional powder hot-pressing methods. Layered TiNiSn microlattices – after 3D ink-extrusion printing and infiltration – exhibit high relative densities and minimal undesirable secondary phase content, with a Seebeck coefficient on par with the ink-cast TiNiSn plates, demonstrating that thermoelectric legs with far-ranging architectural freedom can be created additively with this novel reactive manufacturing method. Numerous other thermoelectric (and other) compounds, currently limited to basic geometries due to brittleness, are amenable to this new method based on a sequence of reactive sintering/infiltration of cast or ink-extruded precursors.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Under-detection of endospore-forming Firmicutes in metagenomic data

Microbial diversity studies based on metagenomic sequencing have greatly enhanced our knowledge of the microbial world. However, one caveat is the fact that not all microorganisms are equally well detected, questioning the universality of this approach. Firmicutes are known to be a dominant bacterial group. Several Firmicutes species are endospore formers and this property makes them hardy in potentially harsh conditions, and thus likely to be present in a wide variety of environments, even as residents and not functional players. While metagenomic libraries can be expected to contain endospore formers, endospores are known to be resilient to many traditional methods of DNA isolation and thus potentially undetectable. In this study we evaluated the representation of endospore-forming Firmicutes in 73 published metagenomic datasets using two molecular markers unique to this bacterial group ( spo0A and gpr ). Both markers were notably absent in well-known habitats of Firmicutes such as soil, with spo0A found only in three mammalian gut microbiomes. A tailored DNA extraction method resulted in the detection of a large diversity of endospore-formers in amplicon sequencing of the 16S rRNA and spo0A genes. However, shotgun classification was still poor with only a minor fraction of the community assigned to Firmicutes . Thus, removing a specific bias in a molecular workflow improves detection in amplicon sequencing, but it was insufficient to overcome the limitations for detecting endospore-forming Firmicutes in whole-genome metagenomics. In conclusion, this study highlights the importance of understanding the specific methodological biases that can contribute to improve the universality of metagenomic approaches.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Multi-level spectral deferred corrections scheme for the shallow water equations on the rotating sphere

Efficient time integration schemes are necessary to capture the complex processes involved in atmospheric flows over long periods of time. We propose a high-order, implicit–explicit numerical scheme that combines Multi-Level Spectral Deferred Corrections (MLSDC) and the Spherical Harmonics (SH) transform to solve the wave-propagation problems arising from the shallow-water equations on the rotating sphere. The iterative temporal integration is based on a sequence of corrections distributed on coupled space–time levels to perform a significant portion of the calculations on a coarse representation of the problem and hence to reduce the time-to-solution while preserving accuracy. In our scheme, referred to as MLSDC-SH, the spatial discretization plays a key role in the efficiency of MLSDC, since the SH basis allows for consistent transfer functions between space–time levels that preserve important physical properties of the solution. We study the performance of the MLSDC-SH scheme with shallow-water test cases commonly used in numerical atmospheric modeling. We use this suite of test cases, which gradually adds more complexity to the nonlinear system of governing partial differential equations, to perform a detailed analysis of the accuracy of MLSDC-SH upon refinement in time. We illustrate the stability properties of MLSDC-SH and show that the proposed scheme achieves up to eighth-order convergence in time. Finally, we study the conditions in which MLSDC-SH achieves its theoretical speedup, and we show that it can significantly reduce the computational cost compared to single-level Spectral Deferred Corrections (SDC).

97 MATHEMATICS AND COMPUTING↗